User: stuart

gravatar for stuart
stuart0
Reputation:
0
Status:
New User
Last seen:
10 months, 1 week ago
Joined:
3 years, 3 months ago
Email:
s************@monash.edu

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by stuart

<prev • 5 results • page 1 of 1 • next >
0
votes
1
answer
244
views
1
answers
Comment: C: Interaction effect sizes from DEXseq
... Ah, I see now, thanks for the clarification. Actually I just realised that mcols(dxrTEST1)$description gives some of this information, but it's useful to know where and when VST is applied too. ...
written 12 months ago by stuart0
0
votes
1
answer
244
views
1
answers
Comment: C: Interaction effect sizes from DEXseq
... Hi Alejandro, Thanks a lot, that's really helpful. Just a related question on the results object, as I want to make sure I genuinely understand how the log2fold-change is calculated: if I set gene_1:exon1 to be upregulated ~10-fold specifically in mut=='A' and treat='trt' by inserting some higher ...
written 12 months ago by stuart0
0
votes
1
answer
244
views
1
answer
Interaction effect sizes from DEXseq
... Dear all, I have a multifactorial experimental design (3 mutants and 2 treatments) am trying to obtain the difference of differences for exon usage. I can obtain p-values but not the fold-change of expression that is attributable to the interaction between mutant and treatment. I hope this makes se ...
dexseq multiple factor design written 12 months ago by stuart0 • updated 12 months ago by Alejandro Reyes1.6k
0
votes
1
answer
722
views
1
answers
Comment: C: Setting contrasts in limma where null hypothesis is that Test = 2 x Control
... Thank you very much, this was really helpful. The duplicated genes show an average ~ +0.8 logFC. This is less than +1.0 probably due to homeostatic mechanisms at play, which indicates that I should treat duplicated genes that are downregulated from the logFC +1.0 baseline with caution. Nonetheless ...
written 3.3 years ago by stuart0
4
votes
1
answer
722
views
1
answer
Setting contrasts in limma where null hypothesis is that Test = 2 x Control
... Hello, I am analysing RNA-seq data to find differentially expressed genes between a wild-type (Ctl) and mutant (Mut). The mutant has a large DNA duplication encompassing several hundred genes, so they always come up as ~2x upregulated but this is not biologically interesting. Hence the H0 (null) fo ...

Latest awards to stuart

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 296 users visited in the last hour